1. Field of the Invention
The present invention relates to systems and methods for examining biological material. In particular, the invention relates to a system, method, and product for generating an interference pattern at the functional surface of a probe array comprising small dimension probe features each having thousands of probe molecules disposed therein. For example, it may be advantageous for systems using biological probe features 1 μm in dimension or smaller to employ specialized methods, optical elements, and/or detection schemes to achieve desired levels of resolution. One such method may be referred to as Patterned Illumination or Patterned Excitation that include generating an interference pattern of excitation light at the surface of a probe array and detecting disturbances in the pattern associated with the probe features. Optical systems have been described to generate interference patterns that include complicated arrays of mirrors, beam splitters, and other components for controlling the pattern including the orientation relative to the probe array, phase, and other characteristics. The presently described invention includes a less complicated, expensive, and sensitive means for generating the interference pattern that employs a pair of adjacent waveguides.
2. Related Art
Synthesized nucleic acid probe arrays, such as Affymetrix GeneChip® probe arrays, and spotted probe arrays, have been used to generate unprecedented amounts of information about biological systems. For example, the GeneChip® Human Genome U133 Plus 2.0 Array available from Affymetrix, Inc. of Santa Clara, Calif., is comprised of one microarray containing 1,300,000 oligonucleotide features covering more than 47,000 transcripts and variants that include 38,500 well characterized human genes. Other examples of GeneChip® arrays are targeted to provide data aimed at different areas of specialization. Examples of specialized uses include analysis of Single Nucleotide Polymorphisms (SNPs) provided by the GeneChip® Human Mapping 10K, 100K, 500K, or 6.0 Arrays, or analysis of alternative splicing events provided by the GeneChip® Human Exon 1.0 ST Array. Analysis of data from such microarrays may lead to the development of new drugs and new diagnostic tools.